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Positive selection identification software tools | Population genomics

Natural selection is a significant force that shapes the architecture of the human genome and introduces diversity across global populations. The question of whether advantageous mutations have arisen in the human genome as a result of single or…
INSIGHT
Web
Desktop
CMS
Desktop

CMS Composite of Multiple Signals

A tool for identifying regions that are under positive selection in the genome…

A tool for identifying regions that are under positive selection in the genome and for localizing the causal variant within these regions. CMS generates a composite score based on three distinct…

HKA
Desktop

HKA

Carries out the widely used statistical test for natural selection. HKA is a…

Carries out the widely used statistical test for natural selection. HKA is a computer program that can handle very large numbers of loci and sample sizes, and conducts tests via coalescent simulation…

Datamonkey
Web

Datamonkey

Implements three complementary methods for detecting sites under selection.…

Implements three complementary methods for detecting sites under selection. Datamonkey is a popular web-based suite of phylogenetic analysis tools for use in evolutionary biology. This web app is…

BALLET
Desktop

BALLET BALancing selection LikElihood Test

Identifies signatures of ancient balancing selection in genetic data. BALLET…

Identifies signatures of ancient balancing selection in genetic data. BALLET models the effect of balancing selection on the genealogy at linked neutral loci and takes into consideration the spatial…

PopGenome
Desktop

PopGenome

A population genomics package for the R software environment (a de facto…

A population genomics package for the R software environment (a de facto standard for statistical analyses). PopGenome can efficiently process genome-scale data as well as large sets of individual…

Selecton
Web

Selecton

Implements an assembly of different evolutionary models, which allow for…

Implements an assembly of different evolutionary models, which allow for statistical testing of the hypothesis that a protein has undergone positive selection. Selecton is a server for detecting…

IDEA
Desktop

IDEA Interactive Display for Evolutionary Analyses

Provides a graphical user interface that allows the user to follow a codeml or…

Provides a graphical user interface that allows the user to follow a codeml or baseml analysis from parameter input through to the exploration of results. IDEA is an intuitive graphical input and…

PhyleasProg
Web

PhyleasProg

Helps to understand, compare and identify the functions of sequences.…

Helps to understand, compare and identify the functions of sequences. PhyleasProg can help biologists by analysing their data in a simple and robust way, using methods corresponding to robust…

MKT
Web

MKT McDonald Kreitman Test

Allows performing McDonald Kreitman Tests (MKTs) not only for synonymous and…

Allows performing McDonald Kreitman Tests (MKTs) not only for synonymous and nonsynonymous changes, as the test was initially described, but also for other classes of regions and/or several loci. The…

POTION
Desktop

POTION POsitive selecTION

Allows users to construct and check hypotheses regarding the occurrence of…

Allows users to construct and check hypotheses regarding the occurrence of site-based evidence of positive selection in non-curated, genome-scale data within a feasible time frame. POTION is an open…

SpectralTDF
Desktop

SpectralTDF Spectral representation of Transition Density Functions

Computes the transition density function (TDF) of the diffusion approximation…

Computes the transition density function (TDF) of the diffusion approximation of the Wright-Fisher process with general diploid selection and recurrent mutation. SpectralTDF program allows for…

WFES
Desktop

WFES Wright-Fisher Exact Solver

Solves for both long term and transient behaviours including fixation and…

Solves for both long term and transient behaviours including fixation and extinction probabilities, expected times to fixation or extinction, sojourn times, expected allele age and variance, and…

PSP
Web

PSP Prokaryotic Selection Pressure

Allows researchers to do genome-scale analysis for evolutionary selection…

Allows researchers to do genome-scale analysis for evolutionary selection across multiple prokaryotic genomes rapidly and easily. PSP is an open access web server, which is designated for performing…

SweeD
Desktop
Web

SweeD Sweep Detector

An open-source tool for the rapid detection of selective sweeps in whole…

An open-source tool for the rapid detection of selective sweeps in whole genomes. SweeD analyzes site frequency spectra and represents a substantial extension of the widely used SweepFinder program.…

iSAFE
Desktop

iSAFE integrated Selection of Allele Favored by Evolution

Pinpoints the favored mutation with population genetics signals and boosting…

Pinpoints the favored mutation with population genetics signals and boosting approach. iSAFE is a method that exploits coalescent based signals to rank all mutations within a 5Mbp around a region…

HaploDistScan
Desktop

HaploDistScan

Permits to detect signals of selection and divergence in comparative genomics.…

Permits to detect signals of selection and divergence in comparative genomics. HaploDistScan is based on the distribution of pair-wise haplotype distances. It is able to detect deep-divergence…

ELS-hmm
Desktop

ELS-hmm

Allows to detect ancient sweeps based on a signal of extended lineage sorting.…

Allows to detect ancient sweeps based on a signal of extended lineage sorting. ELS-hmm is able to detect ancient events of positive selection and can differentiate those from background selection. It…

PosiGene
Desktop

PosiGene

Generates alignment visualizations which enable to contextually interpret the…

Generates alignment visualizations which enable to contextually interpret the positively selected amino acid sites within the respective candidate. PosiGene is a tool that (i) detects positively…

asymptoticMK
Web

asymptoticMK

Provides a simple R-based interface into which the user can upload the required…

Provides a simple R-based interface into which the user can upload the required data (polymorphism and divergence data for the genomic test region and a neutrally evolving reference region).…

Hierarchical…
Desktop

Hierarchical Boosting

A machine-learning classification framework that exploits the combined ability…

A machine-learning classification framework that exploits the combined ability of some selection tests to uncover different polymorphism features expected under the hard sweep model, while…

SweepFinder
Desktop

SweepFinder

Detecting selective sweeps from genomic SNP data is complicated by the…

Detecting selective sweeps from genomic SNP data is complicated by the intricate ascertainment schemes used to discover SNPs, and by the confounding influence of the underlying complex demographics…

HaploPS
Desktop

HaploPS

A long-range-haplotype method for identifying genomic signatures of positive…

A long-range-haplotype method for identifying genomic signatures of positive selection to complement existing methods, such as the integrated haplotype score (iHS) or cross-population extended…

JCoDA
Desktop

JCoDA Java Codon Delimited Alignment

Performs evolutionary analysis on homologous coding sequences. JCoDA is a…

Performs evolutionary analysis on homologous coding sequences. JCoDA is a simple-to-use visualization tool for the detection of site specific and regional positive/negative evolutionary selection…

Haplotter
Web

Haplotter

A web application that has been developed to display the results of a scan for…

A web application that has been developed to display the results of a scan for positive selection in the human genome using the HapMap data. Haplotter can be used as a resource to examine various…

dbCLINE
Web

dbCLINE

A genome-wide scan for evidence of positive selection in response to climatic…

A genome-wide scan for evidence of positive selection in response to climatic variation. dbCLINE allows for the comparison of selection signals from different types of analyses.

evolBoosting
Desktop

evolBoosting

The principle of this package is to use a machine learning method, boosting, to…

The principle of this package is to use a machine learning method, boosting, to study the difference between selected population DNA samples and neutral samples. Then, boosting will produce a…

SFselect
Desktop

SFselect

A method for classifying genomic regions evolving under positive selection,…

A method for classifying genomic regions evolving under positive selection, from those evolving neutrally. We consider a "hard sweep" model of natural selection, where a single (novel)…

ODoSE
Web

ODoSE Ortholog Direction of Selection Engine

Allows the calculation of a novel extension of the McDonald-Kreitman (MK) test,…

Allows the calculation of a novel extension of the McDonald-Kreitman (MK) test, the Direction of Selection (DoS) statistic, as well as the calculation of a weighted-average Neutrality Index (NI)…

OmegaPlus
Desktop

OmegaPlus

An open-source tool for rapid detection of selective sweeps in whole-genome…

An open-source tool for rapid detection of selective sweeps in whole-genome data based on linkage disequilibrium. OmegaPlus is up to two orders of magnitude faster than existing programs for this…

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